Hi again,
I pretty much went about the setting up of afm pulling calculations.
Still I am a little bit concern about the results. When using gmx3.2.1
and applying a Linear removal of the center of mass (i.e. translation) I
see the cell unit still moving during the simulation in a direction
that, looks to me, is opposite to the force I am applying. In fact, when
the pulling rate is smaller, the move is not as dramatic. What am I
doing wrong? I have no note that with 3.3 this doesn't happen. Did
anyone experience something like that?
Any tip/suggestion will be greatly appreciated
Best
M
Marta Murcia wrote:
> Thanks Emily and Maik for your feed-back
> You both are right regarding the init vector. I happened to be the
> sign of it as Emily guessed. Changing the direction by doing
> xpull-xref, ypull -yref, zpull-zref and not xref-xpull.....works
> fine. Thanks for the offer on the script though.
> Thanks Emily for claryfing my confusion on the directional vector
> All the best
> M
>> Maik Goette wrote:
>>> Hi
>>>> There seems to be something wrong with your init-vector.
>> Ich have written a small python script, which simply calculates the
>> vector for convenience purposes. You still need the pull- and
>> COM-group coordinates, though. But that shouldn't be a problem.
>> If you want it, I'll send it via mail.
>>>> Regards
>>>> Maik Goette, Dipl. Biol.
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical & computational biophysics department
>> Am Fassberg 11
>> 37077 Goettingen
>> Germany
>> Tel. : ++49 551 201 2310
>> Fax : ++49 551 201 2302
>> Email : mgoette[at]mpi-bpc.mpg.de
>> mgoette2[at]gwdg.de
>> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/>>>>>> Marta Murcia wrote:
>>>>> Emily,
>>> I just saw your answer
>>> Thanks a lot
>>>>>> I just have another question about the unit vector describing the
>>> direction of pulling. Should it be always a unit vector (1 1 1 for
>>> example)? Should I asumme then that the direction of the pulling is
>>> the one specified by the init vector or could I used that same
>>> vector for example as afm_dir?
>>>>>> Also, I don't know if I am doing something wrong but using afm_ini 1
>>> 1 1 and afm_dir as the vector that connects the two atoms I've
>>> chosen (the pulled and the ref) I am not able to get the spring and
>>> the pulled atom at the same coordinates at the beginning of pull.pdo
>>> file.
>>>>>> # AFM 3.0
>>> # Component selection: 1 1 1
>>> # nSkip 1
>>> # Ref. Group 'm'
>>> # Nr. of pull groups 1
>>> # Group 1 'a_13586' afmVec 1.000000 1.000000 1.000000 AfmRate
>>> 0.020000 AfmK 3000.000000
>>> #####
>>>>>> 0.000000 3.713000 5.627000 5.181000
>>> 3.694000 3.732000 5.712000 5.542000
>>> 4.890000 5.472001
>>>>>> I was able to get it, though, using absolute coordinates leaving the
>>> reference group blanck (using gromac 3.3 since in 3.2.1 there is a
>>> bug on absolute coordinates)
>>>>>> #AFM 3.0
>>> # Component selection: 1 1 1
>>> # nSkip 1
>>> # Ref. Group ''
>>> # Nr. of pull groups 1
>>> # Group 1 'a_13586' afmVec 1.000000 1.000000 1.000000 AfmRate
>>> 0.020000 AfmK 3000.000000
>>> #####
>>> 0.000000 0.000000 0.000000 0.000000
>>> 3.694000 3.694000 5.712000 5.712000
>>> 4.890000 4.890000
>>>>>>>>> what is wrong? am i choosing the wrong starting vector when using a
>>> reference group? (Note that I am using xref-xpull, yref-ypull,
>>> zref-zpull as afm-ini, 0.019 -0.085 0.291)
>>>>>> Again, thanks a lot
>>> M
>>>>>> Emily Walton wrote:
>>>>>>> Hi,
>>>>>>>>> Dear all,
>>>>> I am simulating an unbinding process with the pull code (afm option).
>>>>> I've been reading previous posts about this option and I just
>>>>> wanted to
>>>>> clarify some ideas and ask some questions. There are:
>>>>> 1-The pulling can be done choosing two different molecules. Why a
>>>>> particular group within a molecule can not be used? Not even as a
>>>>> reference group?
>>>>>>>>>>>>>>>>>>>>>>>> Any group that is defined in your index file (specified with mdrun
>>>> - pn pull.ndx) can be used. Look at made_ndx in the manual to learn
>>>> how to add new groups.
>>>>>>>>> 2-Should I need to fixed the center of mass of the protein to avoid
>>>>> shifts? How can I do that? Would it be OK to use posre for the
>>>>> backbone
>>>>> of the protein with carrying out the pulling?
>>>>>>>>>>>>>>>>>>>>>>>> It depends on what you want to do. Typically, something would need
>>>> to be fixed. In ligand-protein systems, the center of mass of the
>>>> protein is a reasonable choice. It was used by Grubmuller et al.
>>>> in their 1996 Science paper on the unbinding of
>>>> biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of
>>>> proteins, one terminal atom may be fixed while the other is pulled.
>>>>>>>> Fixing the center of mass of a group in the index file can be done
>>>> in the .mdp file you feed to grompp. See the manual, chapter 7.
>>>>>>>>> 3-Should I removed all the constraints for the bonds (SHAKE, lincs)?
>>>>>>>>>>>>>>>>>>>>>>>> I think this is a matter of preference. Some people do, some
>>>> people don't. Again, it will depend on your system- is it stable
>>>> without the constraints?
>>>>>>>> The bonds that are broken with afm pulling are bonds described by
>>>> non- bonded interaction terms in gromacs. These bonds wouldn't be
>>>> constrained by shake or lincs anyway, so the presence or absence
>>>> of constrains should have a minimal effect on the simulation results.
>>>>>>>>> 4-once I have the pull.pdo the calculation of the applied force
>>>>> will be
>>>>> F= K*(zspring -zgroup) (assuming I am pulling in the z direction)?
>>>>>>>>>>>>>>>>>>>>>>>> Yes. The spring is an ideal spring, so force is k*(extension). The
>>>> extension can be calculated from the pull.pdo file.
>>>>>>>>>>>> -Emily Walton_______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org>>>>http://www.gromacs.org/mailman/listinfo/gmx-users>>>> Please don't post (un)subscribe requests to the list. Use the www
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>>>>>>>>>>>>>>>>>> _______________________________________________
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